Hi, Rohan.

Sorry to take so long.  You almost have it, but see below.


On Thu, Nov 28, 2013 at 2:12 PM, rohan bareja <rohan_1925@yahoo.co.in>wrote:

> Hi Sean,
>
> Thanks for your help!I am trying to get the gene ids for first 3 gpl list
> objects here, using this:
>
> i). genes_new<- unlist(sapply(gpllist[1:3], function(a) {Table(a)[,'Gene
> ID']}))
>
>
> This is the result of first 3 gene id's in first gpl object(GPL13) using
> the command above.
>
> "1""GPL13"
> "13""GPL13"
> "26""GPL13"
>
> However, I am getting altogether different gene ids's while doing it for
> all 3 gpl objects together as seen above.If I am doing it separately, then
> only i am getting the gene id's which are the correct ones, that I notice
> in gpllist object.
> The count of genes in each case (doing together vs separate )remain same .
>
>
> ii.) genes_new<- unlist(sapply(gpllist[1], function(a) {Table(a)[,'Gene
> ID']}))
>
>
> "818888" "GPL13"
> "821523" "GPL13"
> "824405" "GPL13"
>
>
> genes_new<- unlist(sapply(gpllist[2], function(a) {Table(a)[,'Gene ID']}))
>
> genes_new<- unlist(sapply(gpllist[3], function(a) {Table(a)[,'Gene ID']}))
>
>
>
> Do You know what problem might be here.
>
>
> Thanks,
> Rohan
>
>
>
> On Monday, 25 November 2013 2:33 PM, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
>
>
>
>
>
>
> On Mon, Nov 25, 2013 at 2:22 PM, rohan bareja <rohan_1925@yahoo.co.in>
> wrote:
>
> Hi Sean,
> >
> >the answer was really helpful.I am using this to get all the annotations
> for gpl in this object ,since there are 438 gpl's in annotgpl object.
> >
> >gpllist <- sapply(annotgpl[1:438,1],getGEO,AnnotGPL=TRUE)
>
>
> gpl2geneid = do.call(rbind,lapply(x,function(y)
{return(data.frame(platform=Meta(y)$platform,GeneID=Table(y)[,'Gene
ID']))}))
> head(gpl2geneid)
  platform GeneID
1    GPL13
2    GPL13 818888
3    GPL13 821523
4    GPL13 824405
5    GPL13 840218
6    GPL13 839656




> >But this is a list object, and I am unable to access this using a Table
> function.
> >
> >
>
> Hi, Rohan.
>
> Yes, you'll need to apply the Table() method to each member of the
> gpllist; another sapply or an lapply would be useful here.
>
>
> Sean
>
>
> basically, I would like to have a table with mapping of gpl and all its
> gene ids:
> >
> >GPL 13 geneid1
> >GPL13 geneid2
> >GPL 13 geneid3
> >
> >
> >GPL 14 geneid1
> >GPL14 geneid2
> >GPL 14 geneid3
> >
> >Thanks,
> >Rohan
> >
> >
> >
> >
> >On Friday, 22 November 2013 6:27 PM, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
> >
> >
> >
> >
> >
> >
> >On Fri, Nov 22, 2013 at 4:53 PM, Rohan [guest] <guest@bioconductor.org>
> wrote:
> >
> >
> >>I would like to get the data for all the genes in the form of Gene
> Symbols/Gene ids's mapped to GPL/GSE/GSM/GDS metadata.
> >>I have used GEOmetadb package to get this metadata,however I am not able
> to find a way to extract all this metadata mapped to genes.
> >>
> >>Is their any way GEOquery bioconductor package be used for this?
> >>
> >
> >Good question.  It has a long-winded answer.
> >
> >The GEO platform (GPL) is the only GEO entity that stores any information
> about gene identity.  Other entities (GSM, GSE, GDS) are linked to GPL rows
> by an ID column.  So, to get information about the genes represented by an
> experiment, we need to look at GPL records.  GPL records come in two
> flavors, the submitter-supplied flavor and the so-called "Annotation" GPL
> that has been curated by NCBI GEO.  You'll need to focus on the Annotation
> GPL since those are the ones with a standard "Gene ID" column in all of
> them.  The "Annotation" GPLs are only generated for data sets that have
> been curated by NCBI GEO, namely the GDS records.  So, we need to get the
> distinct GPL records associated with GDS and these will be the entire set
> of "Annotation" GPLs.  Using GEOmetadb (assuming you have already made a
> connection, etc.):
> >
> >annotgpl = dbGetquery(con,"select distinct GPL from gds")
> >
> >Now, annotgpl contains the accession numbers (GPL IDs) for all the
> Annotation GPLs.  You can use these GPL IDs to relate each GPL to GSM, GDS,
> and GSE records.
> >
> >How do you get the information about what genes are on each GPL, though?
>  You'll need to use GEOquery for that.
> >
> >gpl = getGEO(annotgpl[1,1],AnnotGPL=TRUE)
> >
> >gpl is now a GPL object and we can use the Table method to get a data
> frame and grab the Gene ID (which is an Entrez Gene ID):
> >
> >geneids = Table(gpl)[,'Gene ID']
> >
> >Now, you have the Entrez Gene IDs for all features on the platform and
> you can associate those with all the GSM, GDS, and GSE records attached to
> the GPL.  If you loop over all the GPLs in the annotgpl data frame, you'll
> have the information you want, I think.
> >
> >Unfortunately, this is not a complete answer because it does not include
> the submitter-supplied GPLs that do not have any Annotation GPL available
> (since NCBI GEO do not curate everything).  The submitter-supplied GPLs do
> not have a standard vocabulary for what is include in the columns of the
> GPL, so there is not an easy way to automate processing as above.
> >
> >Hope that helps.
> >
> >Sean
> >        [[alternative HTML version deleted]]
> >
> >
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>
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